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Table 4 Highly significant GWAS variants (RMIP ≥ 0.25) and their adjacent candidate genes

From: Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population

Chromosome

Physical position (AGPv2)

Allelea

Effectb

P-value

RMIP

Genic position

Inside QTLc

Nearest gene ID

Position of nearest gene (AGPv2)

Annotation

Start

End

1

59772038

T/C

0.09

9.4E-10

0.35

Intergenicd

N

GRMZM2G134671

59764838

59769739

CCT/B-box zinc finger protein

1

90059294

C/T

0.08

8.5E-14

0.35

Intergenic

Y

GRMZM5G806839

90108398

90107598

AP2 domain containing protein

2

34246559

A/C

0.11

1.8E-16

0.39

Intergenic

N

GRMZM5G876621

34361966

34343251

IBR domain-containing protein

2

36938074

G/A

0.10

1.4E-22

0.53

3’UTR

Y

GRMZM2G022627

36936010

36938218

Transducin/WD40 repeat-like superfamily protein

2

204757213

G/A

0.11

4.5E-09

0.41

Intergenic

N

GRMZM2G142932

204771189

204767728

Basic helix-loop-helix (bHLH) DNA-binding protein

2

207520001

CNV-

0.11

4.4E-09

0.28

Intergenic

Y

GRMZM2G062156

207635000

207637178

Transporter family protein

3

16574125

T/C

0.12

1.8E-26

0.43

Non-synonymous_codinge

Y

GRMZM2G463580

16575869

16572429

Leucine-rich repeat transmembrane protein kinase

3

16575842

C/G

0.15

9.7E-14

0.46

5’UTR

Y

3

32885733

C/T

0.19

9.1E-16

0.9

Intergenic

Y

GRMZM2G132936

32957454

32949608

RNA recognition motif (RRM)-containing protein

3

219885527

T/C

-0.11

3.1E-12

0.28

Intronic

Y

GRMZM2G074572

219900229

219884844

Stomatal cytokinesis defective/SCD1 protein

3

220658469

A/C

-0.08

6.0E-12

0.25

Intronic

Y

GRMZM2G130375

220651805

220659525

Beta galactosidase 1

4

2046350

CGG/---

-0.08

3.8E-09

0.26

Non-synonymous_coding

Y

GRMZM2G131442

2044016

2047386

MYB domain protein 112

5

164110001

CNV-

0.10

1.5E-11

0.42

Intergenic

Y

GRMZM2G111872

164120892

164124546

Heavy metal-associated domain containing protein

6

7001531

A/C

-0.08

1.1E-15

0.4

Intergenic

Y

GRMZM2G127342

7036171

7039824

Lysine histidine transporter 1 (LHT1)

7

7958250

+/-

-0.08

1.9E-08

0.3

Intergenic

Y

GRMZM2G021149

7954180

7955128

LSM domain containing protein

7

142997161

G/A

0.09

7.3E-09

0.28

Intergenic

Y

GRMZM2G091919

143003673

143001781

protein kinase superfamily protein

8

22229116

G/A

0.13

1.3E-08

0.35

Intergenic

N

GRMZM2G325612

22249167

22245141

Cytokinin oxidase 5

8

62217745

T/A

0.10

6.3E-14

0.34

Intergenic

Y

GRMZM2G130101

62267220

62273955

Unknown

8

171334544

A/G

-0.06

1.2E-09

0.26

Intronic

N

GRMZM2G476009

171332654

171335508

DNA-directed RNA polymerases subunit RPABC1

9

16263773

A/G

0.17

9.9E-09

0.33

Intergenic

Y

GRMZM2G301860

16253405

16252231

AP2 domain containing protein

9

16317865

G/A

0.10

1.4E-15

0.59

Down_stream

Y

GRMZM2G099363

16320573

16318197

Caffeoyl-CoA O-methyltransferase

9

106051436

G/A

0.08

1.7E-05

0.45

Intergenic

Y

GRMZM2G107886

106201175

106203143

CCT/B-box zinc finger protein

9

139547728

C/G

-0.11

3.4E-08

0.32

Intergenic

N

GRMZM2G402015

139591514

139589475

Plant U-box 13, spotted leaf 11

10

3090835

G/A

-0.13

6.2E-10

0.47

Intergenic

Y

GRMZM2G068465

3066458

3062645

Cytochrome P450

10

64647379

G/A

0.06

5.7E-09

0.53

Intergenic

Y

NA

   

10

134501142

C/T

0.06

4.4E-08

0.77

Intronic

Y

GRMZM2G063972

134495450

134504022

Heat shock protein DnaJ

  1. aAlleles reported as: “B73 allele/alternate allele”. “CNV-” represents the read depth of a line is significantly lower than B73.
  2. bThe mean effect of each significant SNP across data subsamples.
  3. cSNPs located within model 7 QTL SI are indicated as “Y” and “N” otherwise.
  4. dVariants more than 500 bp away from an annotated gene.
  5. eVariation lies in the coding region and results in an amino acid change.